08 mayo 2022

Introduction

  • Dataset: MiRNA expression in squamous cell carcinoma and adenocarcinoma of the esophagus and associations with survival.

    • Cancerous and noncancerous tissues.
    • Cancer stages.
    • 100 ADC and 70 SCC patients.
    • North American and Japanese cohorts.
    • Other variables (tabacco, alcohol)


  • Objective of the project: To reproduce the findings of the authors and elaborate on their visualizations.

Materials and methods

Materials and methods

Flowchart of the data wrangling and analysis

Results

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Results

Volcano plots

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Results

Differential expression: our findings

Results

Differential expression: author’s findings

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Results

Differential expression: our findings

Results

Differential expression: author’s findings

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Results

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Discussion

  • Data quality: absence of the different North American cohorts hindered the reproducibility of the article.

-Data wrangling: complex data set which required decision-making regarding the selection of relevant probes, NA values, and others.

  • Survival:

  • Differential expression: we weren’t able to reproduce the results, but we found more differentially expressed miRNAs.

  • Principal Component Analysis: